Overall
Plot

Individual metrics
Overall

Batch correction
Batch correction

PCR batch

Batch ASW

Graph iLISI

Graph connectivity

kBET

Bio conservation
Bio conservation

NMI cluster/label

ARI cluster/label

Label ASW

Isolated label F1

Isolated label silhouette

Graph cLISI

HVG conservation

Cell cycle conservation

Trajectory conservation

UMAPs
Full
Scaled
MNN - Features
Batch

Labels

Scanorama - Embedding
Batch

Labels

Scanorama - Features
Batch

Labels

Seurat v3 - Features
Batch

Labels

Harmony - Embedding
Batch

Labels

BBKNN - Graph
Batch

Labels

ComBat - Features
Batch

Labels

FastMNN - Embedding
Batch

Labels

FastMNN - Features
Batch

Labels

Unscaled
MNN - Features
Batch

Labels

Scanorama - Embedding
Batch

Labels

Scanorama - Features
Batch

Labels

Seurat v3 - Features
Batch

Labels

Harmony - Embedding
Batch

Labels

BBKNN - Graph
Batch

Labels

scVI - Embedding
Batch

Labels

ComBat - Features
Batch

Labels

LIGER - Embedding
Batch

Labels

scANVI - Embedding
Batch

Labels

FastMNN - Embedding
Batch

Labels

FastMNN - Features
Batch

Labels

Unintegrated - Features
Batch

Labels

HVG
Scaled
MNN - Features
Batch

Labels

Scanorama - Embedding
Batch

Labels

Scanorama - Features
Batch

Labels

Seurat v3 - Features
Batch

Labels

Harmony - Embedding
Batch

Labels

BBKNN - Graph
Batch

Labels

ComBat - Features
Batch

Labels

FastMNN - Embedding
Batch

Labels

FastMNN - Features
Batch

Labels

Unscaled
MNN - Features
Batch

Labels

Scanorama - Embedding
Batch

Labels

Scanorama - Features
Batch

Labels

Seurat v3 - Features
Batch

Labels

Harmony - Embedding
Batch

Labels

BBKNN - Graph
Batch

Labels

scVI - Embedding
Batch

Labels

ComBat - Features
Batch

Labels

LIGER - Embedding
Batch

Labels

scANVI - Embedding
Batch

Labels

FastMNN - Embedding
Batch

Labels

FastMNN - Features
Batch

Labels
